Searching Molecular Databases with BLAST. Searching Molecular Databases with BLAST. B asic L ocal A lignment S earch T ool How BLAST works Interpreting search results The NCBI Web BLAST interface Demonstration and exercises. Why learn sequence database searching?. What have I cloned ?
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Sorted by E value combinations of query and database sequencesTypical BLAST Output
Is this sequence known? What does it encode?
Choose search program
Each line is a hit combinations of query and database sequences
in the database
by E value
Colored rectangles along the X axis show where in the query sequence
a similarity in the database has been found. Color indicates degree of similarity
Output sorted by E value combinations of query and database sequences
Link to GenBank file combinations of query and database sequences
Link to alignment combinations of query and database sequences
Link to Entrez Gene combinations of query and database sequences
Conserved Domain Search
Conserved domains are shown
graphically. Link to explanation
of the domain.
Blosom 62 is the default BLASTP scoring matrix
4.6 PSI-BLAST is designed for more sensitive protein-protein similarity searches.
Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...".
4.7 PHI-BLAST can do a restricted protein pattern search.
Pattern-Hit Initiated (PHI)-BLAST is designed to search for proteins that contain a pattern specified by the user AND are similar to the query sequence in the vicinity of the pattern. This dual requirement is intended to reduce the number of database hits that contain the pattern, but are likely to have no true homology to the query.